libSBML Python API
5.10.0
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{qual}
qual Implementation of the 'qual' package extention to the Model construct. The extension of SBML Level 3 Core's Model class is relatively straightforward: the Qualitative Models Package adds two lists, one for holding qualitativeSpecies (ListOfQualitativeSpecies), and the other for holding transitions (ListOfTransitions). The Model element may contain at most one ListOfQualitativeSpecies, which must contain at least one QualitativeSpecies. It may also contain at most one ListOfTransitions which must contain at least one Transition.Public Member Functions | |
def | addQualitativeSpecies |
def | addTransition |
def | clone |
def | createQualitativeSpecies |
def | createTransition |
def | getElementByMetaId |
def | getElementBySId |
def | getElementNamespace |
def | getLevel |
def | getListOfAllElements |
def | getListOfQualitativeSpecies |
def | getListOfTransitions |
def | getNumQualitativeSpecies |
def | getNumTransitions |
def | getPackageName |
def | getPackageVersion |
def | getParentSBMLObject |
def | getPrefix |
def | getQualitativeSpecies |
def | getSBMLDocument |
def | getTransition |
def | getURI |
def | getVersion |
def | removeQualitativeSpecies |
def | removeTransition |
def | setElementNamespace |
def libsbml.QualModelPlugin.addQualitativeSpecies | ( | self, | |
args | |||
) |
Python method signature(s):
addQualitativeSpecies(QualModelPlugin self, QualitativeSpecies qualitativeSpecies)int
Adds a copy of the given QualitativeSpecies object to the list of qual.
qualitativeSpecies | the QualitativeSpecies object to be added to the list of qual. |
def libsbml.QualModelPlugin.addTransition | ( | self, | |
args | |||
) |
Python method signature(s):
addTransition(QualModelPlugin self, Transition transition)int
Adds a copy of the given Transition object to the list of qual.
transition | the Transition object to be added to the list of qual. |
def libsbml.QualModelPlugin.clone | ( | self | ) |
{qual}
qual Implementation of the 'qual' package extention to the Model construct. The extension of SBML Level 3 Core's Model class is relatively straightforward: the Qualitative Models Package adds two lists, one for holding qualitativeSpecies (ListOfQualitativeSpecies), and the other for holding transitions (ListOfTransitions). The Model element may contain at most one ListOfQualitativeSpecies, which must contain at least one QualitativeSpecies. It may also contain at most one ListOfTransitions which must contain at least one Transition. Python method signature(s):clone(QualModelPlugin self)QualModelPlugin
Creates and returns a deep copy of this QualModelPlugin object.
def libsbml.QualModelPlugin.createQualitativeSpecies | ( | self | ) |
Python method signature(s):
createQualitativeSpecies(QualModelPlugin self)QualitativeSpecies
Creates a new qual object and adds it to the list of qual objects and returns it.
def libsbml.QualModelPlugin.createTransition | ( | self | ) |
Python method signature(s):
createTransition(QualModelPlugin self)Transition
Creates a new qual object and adds it to the list of qual objects and returns it.
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inherited |
Python method signature(s):
getElementByMetaId(SBasePlugin self, string metaid)SBase
Returns the first child element it can find with the given metaid
, or None
if no such object is found.
metaid | string representing the metaid of objects to find |
metaid
.
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inherited |
Python method signature(s):
getElementBySId(SBasePlugin self, string id)SBase
Returns the first child element found that has the given id
in the model-wide SId namespace, or None
if no such object is found.
id | string representing the id of objects to find |
id
.
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inherited |
{core}
Representation of a plug-in object of SBML's package extension.Additional attributes and/or elements of a package extension which are directly contained by some pre-defined element are contained/accessed by SBasePlugin class which is extended by package developers for each extension point. The extension point, which represents an element to be extended, is identified by a combination of a Package name and a typecode of the element, and is represented by SBaseExtensionPoint class.
For example, the layout extension defines <listOfLayouts> element which is directly contained in <model> element of the core package. In the layout package (provided as one of example packages in libSBML-5), the additional element for the model element is implemented as ListOfLayouts class (an SBase derived class) and the object is contained/accessed by a LayoutModelPlugin class (an SBasePlugin derived class).
SBasePlugin class defines basic virtual functions for reading/writing/checking additional attributes and/or top-level elements which should or must be overridden by subclasses like SBase class and its derived classes.
Package developers must implement an SBasePlugin exntended class for each element to be extended (e.g. SBMLDocument, Model, ...) in which additional attributes and/or top-level elements of the package extension are directly contained.
To implement reading/writing functions for attributes and/or top-level elements of the SBsaePlugin extended class, package developers should or must override the corresponding virtual functions below provided in the SBasePlugin class:
reading elements :
virtual SBase createObject (XMLInputStream stream)
This function must be overridden if one or more additional elements are defined.
virtual bool readOtherXML (SBase parentObject, XMLInputStream stream)
This function should be overridden if elements of annotation, notes, MathML, etc. need to be directly parsed from the given XMLInputStream object.
reading attributes (must be overridden if additional attributes are defined) :
virtual void addExpectedAttributes(ExpectedAttributes& attributes)
virtual void readAttributes (XMLAttributes attributes, ExpectedAttributes& expectedAttributes)
writing elements (must be overridden if additional elements are defined) :
virtual void writeElements (XMLOutputStream stream)
writing attributes :
virtual void writeAttributes (XMLOutputStream stream)
This function must be overridden if one or more additional attributes are defined.
virtual void writeXMLNS (XMLOutputStream stream)
This function must be overridden if one or more additional xmlns attributes are defined.
checking elements (should be overridden) :
virtual bool hasRequiredElements()
checking attributes (should be overridden) :
virtual bool hasRequiredAttributes()
To implement package-specific creating/getting/manipulating functions of the SBasePlugin derived class (e.g., getListOfLayouts(), createLyout(), getLayout(), and etc are implemented in LayoutModelPlugin class of the layout package), package developers must newly implement such functions (as they like) in the derived class.
SBasePlugin class defines other virtual functions of internal implementations such as:
virtual void setSBMLDocument(SBMLDocument d)
virtual void connectToParent(SBasesbase)
virtual void enablePackageInternal(string pkgURI, string pkgPrefix, bool flag)
These functions must be overridden by subclasses in which one or more top-level elements are defined.
For example, the following three SBasePlugin extended classes are implemented in the layout extension:
SBMLDocumentPlugin class for SBMLDocument element
(SBMLDocumentPlugin class is a common SBasePlugin extended class for SBMLDocument class. Package developers can use this class as-is if no additional elements/attributes (except for required attribute) is needed for the SBMLDocument class in their packages, otherwise package developers must implement a new SBMLDocumentPlugin derived class.)
LayoutModelPlugin class for Model element
<listOfLayouts> element is added to Model object.
The following virtual functions for reading/writing/checking are overridden: (type of arguments and return values are omitted)
createObject()
: (read elements) readOtherXML()
: (read elements in annotation of SBML L2) writeElements()
: (write elements) The following virtual functions of internal implementations are overridden: (type of arguments and return values are omitted)
setSBMLDocument()
connectToParent()
enablePackageInternal()
The following creating/getting/manipulating functions are newly implemented: (type of arguments and return values are omitted)
getListOfLayouts()
getLayout ()
addLayout()
createLayout()
removeLayout()
getNumLayouts()
LayoutSpeciesReferencePlugin class for SpeciesReference element (used only for SBML L2V1)
id attribute is internally added to SpeciesReference object only for SBML L2V1
The following virtual functions for reading/writing/checking are overridden: (type of arguments and return values are omitted)
readOtherXML()
writeAttributes()
Python method signature(s):
getElementNamespace(SBasePlugin self)string
Returns the XML namespace (URI) of the package extension of this plugin object.
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inherited |
Python method signature(s):
getLevel(SBasePlugin self)long
Returns the SBML level of the package extension of this plugin object.
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inherited |
def libsbml.QualModelPlugin.getListOfQualitativeSpecies | ( | self, | |
args | |||
) |
Python method signature(s):
getListOfQualitativeSpecies(QualModelPlugin self)ListOfQualitativeSpecies getListOfQualitativeSpecies(QualModelPlugin self)
ListOfQualitativeSpecies
Returns the ListOfQualitativeSpecies in this plugin object.
def libsbml.QualModelPlugin.getListOfTransitions | ( | self, | |
args | |||
) |
Python method signature(s):
getListOfTransitions(QualModelPlugin self)ListOfTransitions getListOfTransitions(QualModelPlugin self)
ListOfTransitions
Returns the ListOfTransitions in this plugin object.
def libsbml.QualModelPlugin.getNumQualitativeSpecies | ( | self | ) |
Python method signature(s):
getNumQualitativeSpecies(QualModelPlugin self)long
Returns the number of QualitativeSpecies object in this plugin object.
def libsbml.QualModelPlugin.getNumTransitions | ( | self | ) |
Python method signature(s):
getNumTransitions(QualModelPlugin self)long
Returns the number of Transition object in this plugin object.
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inherited |
Python method signature(s):
getPackageName(SBasePlugin self)string
Returns the package name of this plugin object.
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inherited |
Python method signature(s):
getPackageVersion(SBasePlugin self)long
Returns the package version of the package extension of this plugin object.
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inherited |
Python method signature(s):
getParentSBMLObject(SBasePlugin self)SBase getParentSBMLObject(SBasePlugin self)
SBase
Returns the parent SBase object to which this plugin object connected.
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inherited |
Python method signature(s):
getPrefix(SBasePlugin self)string
Returns the prefix of the package extension of this plugin object.
def libsbml.QualModelPlugin.getQualitativeSpecies | ( | self, | |
args | |||
) |
Python method signature(s):
getQualitativeSpecies(QualModelPlugin self, long n)QualitativeSpecies getQualitativeSpecies(QualModelPlugin self, long n)
QualitativeSpecies getQualitativeSpecies(QualModelPlugin self, string sid)
QualitativeSpecies getQualitativeSpecies(QualModelPlugin self, string sid)
QualitativeSpecies
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
getQualitativeSpecies(long n)
Returns the QualitativeSpecies object that belongs to the given index. If the index is invalid, None is returned.
n | the index number of the QualitativeSpecies to get. |
getQualitativeSpecies(string sid)
Returns the qualitativeSpecies object based on its identifier.
sid | a string representing the identifier of the QualitativeSpecies to get. |
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inherited |
Python method signature(s):
getSBMLDocument(SBasePlugin self)SBMLDocument getSBMLDocument(SBasePlugin self)
SBMLDocument
Returns the parent SBMLDocument of this plugin object.
def libsbml.QualModelPlugin.getTransition | ( | self, | |
args | |||
) |
Python method signature(s):
getTransition(QualModelPlugin self, long n)Transition getTransition(QualModelPlugin self, long n)
Transition getTransition(QualModelPlugin self, string sid)
Transition getTransition(QualModelPlugin self, string sid)
Transition
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
getTransition(long n)
Returns the Transition object that belongs to the given index. If the index is invalid, None is returned.
n | the index number of the Transition to get. |
getTransition(string sid)
Returns the qualitativeSpecies object based on its identifier.
sid | a string representing the identifier of the Transition to get. |
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inherited |
Python method signature(s):
getURI(SBasePlugin self)string
Gets the URI to which this element belongs to. For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/'
Unlike getElementNamespace, this function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. if not found it will return the result of getElementNamespace
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inherited |
Python method signature(s):
getVersion(SBasePlugin self)long
Returns the SBML version of the package extension of this plugin object.
def libsbml.QualModelPlugin.removeQualitativeSpecies | ( | self, | |
args | |||
) |
Python method signature(s):
removeQualitativeSpecies(QualModelPlugin self, long n)QualitativeSpecies removeQualitativeSpecies(QualModelPlugin self, string sid)
QualitativeSpecies
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
removeQualitativeSpecies(long n)
Removes the nth QualitativeSpecies object from this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the QualitativeSpecies object to remove |
removeQualitativeSpecies(string sid)
Removes the QualitativeSpecies object with the given id attribute from this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
sid | the id attribute of the QualitativeSpecies object to remove |
def libsbml.QualModelPlugin.removeTransition | ( | self, | |
args | |||
) |
Python method signature(s):
removeTransition(QualModelPlugin self, long n)Transition removeTransition(QualModelPlugin self, string sid)
Transition
This method has multiple variants that differ in the arguments they accept. Each is described separately below.
removeTransition(long n)
Removes the nth Transition object from this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
n | the index of the Transition object to remove |
removeTransition(string sid)
Removes the Transition object with the given id attribute from this plugin object and returns a pointer to it.
The caller owns the returned object and is responsible for deleting it.
sid | the id attribute of the Transition object to remove |
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inherited |
Python method signature(s):
setElementNamespace(SBasePlugin self, string uri)int
Sets the XML namespace to which this element belongs to. For example, all elements that belong to SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/layout/version1/'